I've noticed a several hundred dollar difference in prices between the Amtrak website and the Amtrak iPhone App for a 2-person reservation. I have a reservation from NYP-CHI on the LSL, continuing on the EB #27 from CHI to PDX. My original reservation was made sometime in January.
I frequently check the fares to see if they change. When I checked the prices on both sites a few days ago, I noticed the difference in fares. I called the 800 number and talked to an agent, I ended up with a totally different fare than either site. Then, for some reason, the bedrooms prices were cheaper than the roomette prices on the EB. They ended up changing my reservation, I got a $92 refund and switched from a Roomette to a Bedroom on the EB. (The website said no more roomettes were available at that time). The next day I rechecked the fares again, and the roomettes were now down to $243 and the bedrooms were $802. However, there is still a $369 difference in price between the website and the app for a 2-person reservation.